if i were you...I would have just gone over the frame with a scotch brite pad to remove as much loose rust and paint as you can(not down to bare metal) and then clear over the rust and old paint.
this would have preserved the original finish and give the bike the "patina look" that everyone is after. But, it;s your bike, not mine.

If you have polished the bare metal of the frame and if you're going to clear coat it, you should use some wax and grease remover on the metal before you clear it.
the clear may not stick because of the polishing compound.

Definitely! I was planning on using either a Simple Green & water solution, or dish soap & water before clearing.